Contents

• 1. Introduction
  • 1.1 Road Map
  • 1.2 Help
    • 1.2.1 Documentation Distribution
    • 1.2.2 The Web
    • 1.2.3 Mailing Lists
  • 1.3 Reporting Bugs
  
  
• 2. Concepts
  • 2.1 Traditional Problem Solving Methods
  • 2.2 Integrated Problem Solving and Computational Steering
    • 2.2.1 SCIRun and its Packages
  • 2.3 SCIRun Modules, Networks, and Sub-Networks
  • 2.4 SCIRun's Use of Third Party Software
    • 2.4.1 Matlab Interface
    • 2.4.2 Insight Tool Kit
    • 2.4.3 PETSc
    • 2.4.4 GENESIS (via SQL)
  • 2.5 Extensibility
  • 2.6 Power Apps
  • 2.7 SCIRun Objects
    • 2.7.1 Field
    • 2.7.2 Field Data
    • 2.7.3 Meshes
    • 2.7.4 Matrices
    • 2.7.5 Color Map
  • 2.8 Bioelectric Field Quantities and Units
  
  
• 3. Packages
  • 3.1 SCIRun Core
  • 3.2 BioPSE
  • 3.3 Teem
  • 3.4 MatlabInterface
  • 3.5 Insight (ITK)
  • 3.6 DataIO
  
  
• 4. Starting SCIRun
  • 4.1 Preparation
  • 4.2 Anatomy of the Main Window
  • 4.3 The Terminal Window
  • 4.4 SCIRun's Initialization File--.scirunrc
  • 4.5 Remote Display
  • 4.6 Dynamic Compilation
  • 4.7 Exiting SCIRun
  
  
• 5. Working with Networks
  • 5.1 Anatomy of a Module
  • 5.2 Anatomy of a Connection
  • 5.3 Creating a Module
  • 5.4 Setting Module Properties
  • 5.5 Selecting Modules
  • 5.6 Destroying Modules
  • 5.7 Moving Modules
  • 5.8 Disabling and Enabling Modules
  • 5.9 Editing and Displaying Module Notes
  • 5.10 Viewing a Module's Log
  • 5.11 Creating a Connection
  • 5.12 Editing and Displaying Connection Notes
  • 5.13 Highlighting Related Connections
  • 5.14 Disabling a Connection
  • 5.15 Deleting a Connection
  • 5.16 Undoing/Redoing a Connection
  • 5.17 Executing a Network
    • 5.17.1 The Basics
    • 5.17.2 Details
    • 5.17.3 Intermediate Results
    • 5.17.4 Feedback Loops
  • 5.18 Documenting a Network
  • 5.19 Saving a Network
  • 5.20 Loading a Network
  • 5.21 Inserting a Network
  • 5.22 Clearing a Network
  • 5.23 Navigating a Network
  • 5.24 Creating a Sub-Network
  • 5.25 Expanding a Sub-Network
  • 5.26 Editing a Sub-Network
  • 5.27 Saving a Sub-network
  • 5.28 Loading a Sub-Network
  • 5.29 The SCIRun Shell
  
  
• 6. Visualization
  • 6.1 Anatomy of the Viewer Window
    • 6.1.1 Menus
  • 6.2 Recording Movies
  • 6.3 Mouse Control in the Viewer Window
  • 6.4 Extended Control Window
    • 6.4.1 Rendering Controls
    • 6.4.2 Object Selection and Settings
    • 6.4.3 Miscellaneous Settings
  • 6.5 Control Widgets
    • 6.5.1 Point Widget
    • 6.5.2 Rake Widget
    • 6.5.3 Frame Widget
    • 6.5.4 Box Widget
    • 6.5.5 Ring Widget
  
  
• 7. Importing and Exporting SCIRun Data
  • 7.1 Using Readers
  • 7.2 Using Writers
  • 7.3 Text-based File Formats
    • 7.3.1 Node Coordinate File
    • 7.3.2 Connectivity Files
    • 7.3.3 Structured Meshes
    • 7.3.4 Column Matrix
    • 7.3.5 Dense Matrix
    • 7.3.6 Sparse Row Matrix
    • 7.3.7 Color Map
  
  
• 8. Wrapping ITK Filters in SCIRun Modules
  • 8.1 Aim
  • 8.2 Approach
  • 8.3 ITK Filter Description
    • 8.3.1 Element <filter-itk>
    • 8.3.2 Element <description>
    • 8.3.3 Element <templated>
    • 8.3.4 Element <datatypes>
    • 8.3.5 Element <inputs>
    • 8.3.6 Element <outputs>
    • 8.3.7 Element <parameters>
    • 8.3.8 Element <includes>
  • 8.4 SCIRun Filter Description
    • 8.4.1 Element <filter>
    • 8.4.2 Element <include>
    • 8.4.3 Element <filter-sci>
  • 8.5 SCIRun GUI Description
  • 8.6 Putting It All Together
  • 8.7 Examples
  
  
• Bibliography
• Index